This is a tutorial to guide the analysis of RNAseq datasets using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL.
For details instructions to setup the transcriptutorial (data, software, R packages, etc), visit INSTALL.md.
This tutorial is split into several sections, from normalisation to causal network analysis. Once set up, you may run each step sequentially. The corresponding R markdown scripts for each of those sections can be found in the scripts subfolder.
Pathway activity with Progeny
Trascription factors activity with Dorothea/Viper
Network reconstruction with CARNIVAL
Analysis of CARNIVAL results
For any question/suggestions, we encourage you to use the issue submission system :)